ArduPilot

The ArduPilot project is a family of open source autopilots based on the Arduino open source computing platform. It consists of a choice of ArduPilot Mega (APM) electronics and a range of free software versions for different vehicles

APM 2.6 is a pro-quality IMU autopilot based on the Arduino Mega platform, which can turn any RC vehicle into a fully autonomous Unmanned Aerial (or Ground) Vehicle. Depending on which software you choose, it can fly fixed-wing aircraft, multicopters, helicopters, and control ground rovers and boats. It handles both autonomous stabilization and GPS navigation and allows fully scripted waypoint missions and camera control. It supports 8 RC channels, has four serial ports and features an all-in design.

You can buy APM 2.5 for $159 ($240 with advanced GPS module) here. Everything else you need for a complete autopilot (flight software and desktop utility software) is free!

Simple setup process and firmware loading via a point-and-click utility. No programming required! (But if you do want to fiddle with the code, you can with the easiest embedded programming toolkit available: Arduino)

Full mission scripting with point-and-click desktop utilities

Can support hundreds of 3D waypoints

Two-way telemetry and in-flight command using the powerful MAVLink protocol